[2024-01-24 13:21:11,068] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:11,070] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:11,070] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a07099a-9591-4d89-b6ca-55b3a66ec979/dqc_reference
[2024-01-24 13:21:12,242] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:12,242] [INFO] Task started: Prodigal
[2024-01-24 13:21:12,243] [INFO] Running command: gunzip -c /var/lib/cwl/stgc84e4879-bcbf-459e-98a1-1e9d79aa3c9c/GCF_014055025.1_ASM1405502v1_genomic.fna.gz | prodigal -d GCF_014055025.1_ASM1405502v1_genomic.fna/cds.fna -a GCF_014055025.1_ASM1405502v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:19,984] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:19,984] [INFO] Task started: HMMsearch
[2024-01-24 13:21:19,984] [INFO] Running command: hmmsearch --tblout GCF_014055025.1_ASM1405502v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a07099a-9591-4d89-b6ca-55b3a66ec979/dqc_reference/reference_markers.hmm GCF_014055025.1_ASM1405502v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:20,206] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:20,207] [INFO] Found 6/6 markers.
[2024-01-24 13:21:20,236] [INFO] Query marker FASTA was written to GCF_014055025.1_ASM1405502v1_genomic.fna/markers.fasta
[2024-01-24 13:21:20,237] [INFO] Task started: Blastn
[2024-01-24 13:21:20,237] [INFO] Running command: blastn -query GCF_014055025.1_ASM1405502v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a07099a-9591-4d89-b6ca-55b3a66ec979/dqc_reference/reference_markers.fasta -out GCF_014055025.1_ASM1405502v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:21,079] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:21,083] [INFO] Selected 16 target genomes.
[2024-01-24 13:21:21,084] [INFO] Target genome list was writen to GCF_014055025.1_ASM1405502v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:21,098] [INFO] Task started: fastANI
[2024-01-24 13:21:21,098] [INFO] Running command: fastANI --query /var/lib/cwl/stgc84e4879-bcbf-459e-98a1-1e9d79aa3c9c/GCF_014055025.1_ASM1405502v1_genomic.fna.gz --refList GCF_014055025.1_ASM1405502v1_genomic.fna/target_genomes.txt --output GCF_014055025.1_ASM1405502v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:21:38,254] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:38,254] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a07099a-9591-4d89-b6ca-55b3a66ec979/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:21:38,255] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a07099a-9591-4d89-b6ca-55b3a66ec979/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:21:38,268] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:21:38,268] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:21:38,268] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Neisseria bacilliformis	strain=DSM 23338	GCA_014055025.1	267212	267212	type	True	100.0	828	830	95	conclusive
Neisseria bacilliformis	strain=ATCC BAA-1200	GCA_000194925.1	267212	267212	type	True	99.9189	811	830	95	conclusive
Kingella potus	strain=NCTC13336	GCA_900451175.1	265175	265175	type	True	86.9177	628	830	95	below_threshold
Kingella potus	strain=3/SID/1128	GCA_022870985.1	265175	265175	type	True	86.7795	626	830	95	below_threshold
Neisseria elongata	strain=NCTC10660	GCA_900453895.1	495	495	type	True	81.8027	472	830	95	below_threshold
Neisseria elongata subsp. elongata	strain=ATCC 25295	GCA_900113545.1	214482	495	type	True	81.6709	466	830	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_022749515.1	1056807	1056807	type	True	80.4707	365	830	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_000813705.1	1056807	1056807	type	True	80.4094	347	830	95	below_threshold
Eikenella longinqua	strain=NML02-A-017	GCA_001648355.1	1795827	1795827	type	True	80.3133	365	830	95	below_threshold
Neisseria cinerea	strain=CCUG 2156	GCA_021025975.1	483	483	type	True	79.804	264	830	95	below_threshold
Neisseria meningitidis	strain=PartJ-Nmeningitidis-RM8376	GCA_022869645.1	487	487	type	True	79.7741	327	830	95	below_threshold
Bergeriella denitrificans	strain=NBRC 102155	GCA_001592185.1	494	494	type	True	79.7131	315	830	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	79.0888	320	830	95	below_threshold
Neisseria dumasiana	strain=93087	GCA_002108505.1	1931275	1931275	type	True	78.9757	307	830	95	below_threshold
Uruburuella suis	strain=1258/02	GCA_022870845.1	252130	252130	type	True	78.697	369	830	95	below_threshold
Uruburuella suis	strain=DSM 17474	GCA_004341385.1	252130	252130	type	True	78.5884	348	830	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:21:38,270] [INFO] DFAST Taxonomy check result was written to GCF_014055025.1_ASM1405502v1_genomic.fna/tc_result.tsv
[2024-01-24 13:21:38,271] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:21:38,271] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:21:38,271] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a07099a-9591-4d89-b6ca-55b3a66ec979/dqc_reference/checkm_data
[2024-01-24 13:21:38,272] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:21:38,302] [INFO] Task started: CheckM
[2024-01-24 13:21:38,302] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014055025.1_ASM1405502v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014055025.1_ASM1405502v1_genomic.fna/checkm_input GCF_014055025.1_ASM1405502v1_genomic.fna/checkm_result
[2024-01-24 13:22:06,651] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:06,652] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:06,676] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:06,676] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:06,676] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014055025.1_ASM1405502v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:06,677] [INFO] Task started: Blastn
[2024-01-24 13:22:06,677] [INFO] Running command: blastn -query GCF_014055025.1_ASM1405502v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a07099a-9591-4d89-b6ca-55b3a66ec979/dqc_reference/reference_markers_gtdb.fasta -out GCF_014055025.1_ASM1405502v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:08,287] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:08,290] [INFO] Selected 18 target genomes.
[2024-01-24 13:22:08,290] [INFO] Target genome list was writen to GCF_014055025.1_ASM1405502v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:08,302] [INFO] Task started: fastANI
[2024-01-24 13:22:08,302] [INFO] Running command: fastANI --query /var/lib/cwl/stgc84e4879-bcbf-459e-98a1-1e9d79aa3c9c/GCF_014055025.1_ASM1405502v1_genomic.fna.gz --refList GCF_014055025.1_ASM1405502v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014055025.1_ASM1405502v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:25,507] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:25,522] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:25,522] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_014055025.1	s__Neisseria bacilliformis	100.0	827	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.33	96.96	0.94	0.89	4	conclusive
GCF_900451175.1	s__Neisseria potus	86.908	630	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237445.1	s__Neisseria sp002237445	86.6306	577	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.69	99.69	0.98	0.98	2	-
GCA_905372165.1	s__CAJPNX01 sp905372165	81.0642	353	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__CAJPNX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005886145.1	s__Neisseria sp000090875	80.5745	392	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.69	97.41	0.97	0.94	3	-
GCF_017753665.1	s__Neisseria sicca_D	80.4704	353	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.2415	96.44	95.35	0.92	0.88	6	-
GCF_014054945.1	s__Neisseria sicca	80.3648	381	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5569	99.97	99.97	1.00	1.00	2	-
GCF_001648475.1	s__Eikenella halliae	80.3632	359	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001648355.1	s__Eikenella longinqua	80.3609	362	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001809325.1	s__Neisseria sp001809325	80.355	349	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.406	N/A	N/A	N/A	N/A	1	-
GCF_000952795.1	s__Neisseria sp000952795	80.2553	342	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.4916	98.25	96.69	0.90	0.83	3	-
GCA_001067655.1	s__Neisseria lactamica_B	80.209	314	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.406	N/A	N/A	N/A	N/A	1	-
GCF_000227275.1	s__Neisseria sp000227275	80.1832	380	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.3387	97.52	96.71	0.95	0.93	3	-
GCF_002216145.1	s__Neisseria chenwenguii	80.1496	404	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.73	99.73	0.96	0.96	2	-
GCF_003044455.1	s__Neisseria bergeri	79.7238	310	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.18	96.14	0.94	0.92	5	-
GCF_001592185.1	s__Neisseria denitrificans	79.6959	317	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002108505.1	s__Neisseria dumasiana	79.0514	304	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.54	97.26	0.91	0.89	4	-
GCF_004341385.1	s__Neisseria suis	78.5275	355	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.29	97.17	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:25,523] [INFO] GTDB search result was written to GCF_014055025.1_ASM1405502v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:25,524] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:25,528] [INFO] DFAST_QC result json was written to GCF_014055025.1_ASM1405502v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:25,528] [INFO] DFAST_QC completed!
[2024-01-24 13:22:25,528] [INFO] Total running time: 0h1m14s